Data from: Historical processes and contemporary ocean currents drive genetic structure in the seagrass Thalassia hemprichii in the Indo-Australian Archipelago

Understanding spatial patterns of gene flow and genetic structure is essential for the conservation of marine ecosystems. Contemporary ocean currents and historical isolation due to Pleistocene sea-level fluctuations have been predicted to influence the genetic structure in marine populations. In the Indo-Australian Archipelago (IAA), the world's hotspot of marine biodiversity, seagrasses are a vital component but population genetic information is very limited. Here, we reconstructed the phylogeography of the seagrass Thalassia hemprichii in the IAA based on single nucleotide polymorphisms (SNPs) and then characterised the genetic structure based on a panel of 16 microsatellite markers. We further examined the relative importance of historical isolation and contemporary ocean currents in driving the patterns of genetic structure. Results from SNPs revealed three population groups: eastern Indonesia, western Indonesia (Sunda Shelf), and Indian Ocean; while the microsatellites supported five population groups (eastern Indonesia, Sunda Shelf, Lesser Sunda, Western Australia, and Indian Ocean). Both SNPs and microsatellites showed asymmetrical gene flow among population groups with a trend of south-westward migration from eastern Indonesia. Genetic diversity was generally higher in eastern Indonesia and decreased southwestward. The pattern of genetic structure and connectivity is attributed partly to the Pleistocene sea level fluctuations modified to a smaller level by contemporary ocean currents.解析基因流的空间格局与种群遗传结构，对于海洋生态系统的保护至关重要。现有洋流以及更新世（Pleistocene）海平面波动引发的历史隔离效应，被认为会影响海洋种群的遗传结构。作为全球海洋生物多样性热点区域的印度-澳大利亚群岛（Indo-Australian Archipelago，简称IAA）内，海草是关键生态组成部分，但相关种群遗传信息极为匮乏。本研究基于单核苷酸多态性（single nucleotide polymorphisms，简称SNPs）标记，重构了印度-澳大利亚群岛内海神草（Thalassia hemprichii）的系统地理学格局，并通过16个微卫星标记（microsatellite markers）组合解析其种群遗传结构。本研究进一步探究了历史隔离与现有洋流在塑造种群遗传结构过程中的相对重要性。单核苷酸多态性分析结果显示存在3个种群集群：印尼东部、印尼西部的巽他陆架（Sunda Shelf）以及印度洋；而微卫星标记则识别出5个种群集群：印尼东部、巽他陆架（Sunda Shelf）、小巽他群岛（Lesser Sunda）、西澳大利亚（Western Australia）以及印度洋。单核苷酸多态性与微卫星标记均显示种群集群间存在不对称基因流，且呈现出从印尼东部向西南方向迁移的趋势。种群遗传多样性整体以印尼东部为最高，并向西南方向逐渐降低。该种群遗传结构与连通性格局，部分归因于更新世海平面波动，而现有洋流仅对该格局产生了较弱的调控作用。